Create an evidence plot for a module

Usage

evidencePlot(
  l,
  m,
  mset = "all",
  rug = TRUE,
  roc = TRUE,
  filter = FALSE,
  unique = TRUE,
  add = FALSE,
  col = "black",
  col.rug = "#eeeeee",
  gene.labels = NULL,
  gene.colors = NULL,
  gene.lines = 1,
  gl.cex = 1,
  style = "roc",
  lwd = 1,
  lty = 1,
  rug.size = 0.2,
  legend = NULL,
  ...
)

Arguments

l: sorted list of HGNC gene identifiers
m: character vector of modules for which the plot should be created
mset: Which module set to use (see tmodUtest for details)
rug: if TRUE, draw a rug-plot beneath the ROC curve
roc: if TRUE, draw a ROC curve above the rug-plot
filter: if TRUE, genes not defined in the module set will be removed
unique: if TRUE, duplicates will be removed
add: if TRUE, the plot will be added to the existing plot
col: a character vector color to be used
col.rug: a character value specifying the color of the rug
gene.labels: if TRUE, gene names are shown; alternatively, a named character vector with gene labels to be shown, or NULL (default) for no labels (option evaluated only if rug is plotted)
gene.colors: NULL (default) or a character vectors indicating the color for each gene. Either a named vector or a vector with the same order of genes as `l`.
gene.lines: a number or a vector of numbers; line width for marking the genes on the rug (default=1). If the vector is named, the names should be gene ids.
gl.cex: Text cex (magnification) for gene labels
style: "roc" for receiver-operator characteristic curve (default), and "gsea" for GSEA-style (Kaplan-Meier like plot)
lwd: line width (see par())
lty: line type (see par())
rug.size: fraction of the plot that should show the rug. If rug.size is 0, rug is not drawn. If rug.size is 1, ROC curve is not drawn.
legend: position of the legend. If NULL, no legend will be drawn
...: Further parameters passed to the plotting function

Details

This function creates an evidence plot for a module, based on an ordered list of genes. By default, the plot shows the receiving operator characteristic (ROC) curve and a rug below, which indicates the distribution of the module genes in the sorted list.

Several styles of the evidence plot are possible: * roc (default): a receiver-operator characteristic like curve; the area under the curve corresponds to the effect size (AUC) * roc_absolute: same as above, but the values are not scaled by the total number of genes in a module * gsea * enrichment: the curve shows relative enrichment at the given position

Examples

# artificially enriched list of genes
set.seed(123)
data(tmod)
bg <- sample(tmod$gv)
fg <- getGenes("LI.M127", as.list=TRUE)[[1]]
fg <- sample(c(fg, bg[1:1000]))
l <- unique(c(fg, bg))
evidencePlot(l, "LI.M127")
evidencePlot(l, filter=TRUE, "LI.M127")

Create an evidence plot for a module

Usage

Arguments

Details

See also

Examples